Locus 13044

Sequence ID dm3.chrX
Location 4,049,602 – 4,049,748
Length 146
Max. P 0.944342
window17926 window17927 window17928

overview

Window 6

Location 4,049,602 – 4,049,714
Length 112
Sequences 4
Columns 117
Reading direction forward
Mean pairwise identity 92.22
Shannon entropy 0.12441
G+C content 0.30566
Mean single sequence MFE -24.55
Consensus MFE -18.80
Energy contribution -21.30
Covariance contribution 2.50
Combinations/Pair 1.03
Mean z-score -2.20
Structure conservation index 0.77
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.50
SVM RNA-class probability 0.720002
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 4049602 112 + 22422827
UAAAUUAUAGUUGUUAUUAUUUUCCUUCCAUGAAUGCUUAU--UGGUUGCUUUCAUGUGAAGCCUGUUAACGAUUUUAACGACAAAAUGUC---CGUUGAUUGCGUUUUAUGUGAAA
....(((((...............((((((((((.((....--.....)).)))))).))))......((((...((((((((.....)).---))))))...))))...))))).. ( -22.60, z-score =  -1.95, R)
>droSim1.chrX 3022803 116 + 17042790
UAAAUUAUUGUUGUUAAUAUUUUCAUUCCAUGAAUGCUUAUAUUGGUUGCUUUCAUAUGAAGCCUGUUAAC-AUUUUAACGACAAGUUGUCGUCCGUUGAUUGCGUUUUAUGUGAAA
.........((..(((((((...(((((...)))))...)))))))..)).(((((((((((((.((((((-......(((((.....)))))..)))))).).)))))))))))). ( -28.40, z-score =  -3.27, R)
>droSec1.super_4 3506032 116 - 6179234
UAAAUUAUUGUUGUUAAUAUUUUCAUUCCAUGAAUGCUUAUAUUGGUUGCUUUCAUAUGAAGCCUGUUAAC-AUUUUAACGACAAGUUGUCGUUCGUUGAUUGCGUUUUAUGUGAAA
.........((..(((((((...(((((...)))))...)))))))..)).(((((((((((((.((((((-.....((((((.....)))))).)))))).).)))))))))))). ( -29.60, z-score =  -3.61, R)
>droEre2.scaffold_4690 1426598 111 + 18748788
UAAAUUAUUGUUGUUAUUAUAUUCUGUCCAUGAAUGCUUAU--UGGUUGCUUUCAUGUGAAGCCUGUUAAC-AUUUUAACGACAACUUGUC---CGUUGAUUGCGUUUUAUGUGAAA
...........(((((..(((..((.((((((((.((....--.....)).)))))).))))..)))))))-)..((((((((.....)).---))))))(..(((...)))..).. ( -17.60, z-score =   0.01, R)
>consensus
UAAAUUAUUGUUGUUAAUAUUUUCAUUCCAUGAAUGCUUAU__UGGUUGCUUUCAUAUGAAGCCUGUUAAC_AUUUUAACGACAAGUUGUC___CGUUGAUUGCGUUUUAUGUGAAA
.........((..(((((((...(((((...)))))...)))))))..)).(((((((((((((.((((((.......(((((.....)))))..)))))).).)))))))))))). (-18.80 = -21.30 +   2.50)

alignment

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secondary structure

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dotplot

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Window 7

Location 4,049,602 – 4,049,714
Length 112
Sequences 4
Columns 117
Reading direction reverse
Mean pairwise identity 92.22
Shannon entropy 0.12441
G+C content 0.30566
Mean single sequence MFE -17.70
Consensus MFE -14.93
Energy contribution -15.17
Covariance contribution 0.25
Combinations/Pair 1.04
Mean z-score -1.89
Structure conservation index 0.84
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.58
SVM RNA-class probability 0.750583
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 4049602 112 - 22422827
UUUCACAUAAAACGCAAUCAACG---GACAUUUUGUCGUUAAAAUCGUUAACAGGCUUCACAUGAAAGCAACCA--AUAAGCAUUCAUGGAAGGAAAAUAAUAACAACUAUAAUUUA
((((......((((.....((((---.((.....)))))).....))))......((((.((((((.((.....--....)).)))))))))))))).................... ( -19.30, z-score =  -2.73, R)
>droSim1.chrX 3022803 116 - 17042790
UUUCACAUAAAACGCAAUCAACGGACGACAACUUGUCGUUAAAAU-GUUAACAGGCUUCAUAUGAAAGCAACCAAUAUAAGCAUUCAUGGAAUGAAAAUAUUAACAACAAUAAUUUA
(((((........((....((((((((((.....))))))....)-))).....))(((.((((((.((...........)).)))))))))))))).................... ( -17.80, z-score =  -1.59, R)
>droSec1.super_4 3506032 116 + 6179234
UUUCACAUAAAACGCAAUCAACGAACGACAACUUGUCGUUAAAAU-GUUAACAGGCUUCAUAUGAAAGCAACCAAUAUAAGCAUUCAUGGAAUGAAAAUAUUAACAACAAUAAUUUA
(((((........((....((((((((((.....))))))....)-))).....))(((.((((((.((...........)).)))))))))))))).................... ( -17.40, z-score =  -1.78, R)
>droEre2.scaffold_4690 1426598 111 - 18748788
UUUCACAUAAAACGCAAUCAACG---GACAAGUUGUCGUUAAAAU-GUUAACAGGCUUCACAUGAAAGCAACCA--AUAAGCAUUCAUGGACAGAAUAUAAUAACAACAAUAAUUUA
..........((((....((((.---.....)))).))))....(-((((.....((((.((((((.((.....--....)).)))))))).)).......)))))........... ( -16.30, z-score =  -1.47, R)
>consensus
UUUCACAUAAAACGCAAUCAACG___GACAACUUGUCGUUAAAAU_GUUAACAGGCUUCACAUGAAAGCAACCA__AUAAGCAUUCAUGGAAUGAAAAUAAUAACAACAAUAAUUUA
((((.........((...........(((.....)))(((((.....)))))..))(((.((((((.((...........)).))))))))).)))).................... (-14.93 = -15.17 +   0.25)

alignment

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secondary structure

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dotplot

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Window 8

Location 4,049,639 – 4,049,748
Length 109
Sequences 5
Columns 114
Reading direction forward
Mean pairwise identity 92.58
Shannon entropy 0.12518
G+C content 0.30227
Mean single sequence MFE -22.94
Consensus MFE -19.34
Energy contribution -19.14
Covariance contribution -0.20
Combinations/Pair 1.07
Mean z-score -2.45
Structure conservation index 0.84
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.50
SVM RNA-class probability 0.944342
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 4049639 109 + 22422827
--UUAUUGGUUGCUUUCAUGUGAAGCCUGUUAACGAUUUUAACGACAAAAUGUC---CGUUGAUUGCGUUUUAUGUGAAAUACUGUAACAAUUAAAAAUCAUCAAUUUUCCUCU
--......(((((((((((((((((((.(((((((........(((.....)))---))))))).).)))))))))))))....)))))......................... ( -23.00, z-score =  -2.43, R)
>droSim1.chrX 3022840 113 + 17042790
UUAUAUUGGUUGCUUUCAUAUGAAGCCUGUUAAC-AUUUUAACGACAAGUUGUCGUCCGUUGAUUGCGUUUUAUGUGAAAUACUGUAACAAUUAAAAAUCAUCAAUUUUCCUCU
........(((((((((((((((((((.((((((-......(((((.....)))))..)))))).).)))))))))))))....)))))......................... ( -25.90, z-score =  -3.20, R)
>droSec1.super_4 3506069 113 - 6179234
UUAUAUUGGUUGCUUUCAUAUGAAGCCUGUUAAC-AUUUUAACGACAAGUUGUCGUUCGUUGAUUGCGUUUUAUGUGAAAUACUGUAACAAUUAAAAAUCAUCAAUUUUCCUCU
........(((((((((((((((((((.((((((-.....((((((.....)))))).)))))).).)))))))))))))....)))))......................... ( -27.10, z-score =  -3.53, R)
>droYak2.chrX 17391207 107 - 21770863
--UUAUUGGUUGCUUUCAUGUGAAGCUUGUUAAC-AUUUUAACGACAACUUGUC---CGUUGAUUGCAUUUUAUGUGAAAUACUGUAACAAUUAAAAAUCAUUA-UUUUCCUCU
--......(((((((((((((((((((((((((.-...)))))))((((.....---.))))...))..)))))))))))....)))))...............-......... ( -18.40, z-score =  -1.22, R)
>droEre2.scaffold_4690 1426635 107 + 18748788
--UUAUUGGUUGCUUUCAUGUGAAGCCUGUUAAC-AUUUUAACGACAACUUGUC---CGUUGAUUGCGUUUUAUGUGAAAUAAUGUAACAAUUAAAAAUCAUUA-UUUUCCUCU
--......((((((((((((((((((.((((((.-...)))))).((((.....---.)))).....)))))))))))))....)))))...............-......... ( -20.30, z-score =  -1.85, R)
>consensus
__UUAUUGGUUGCUUUCAUGUGAAGCCUGUUAAC_AUUUUAACGACAACUUGUC___CGUUGAUUGCGUUUUAUGUGAAAUACUGUAACAAUUAAAAAUCAUCAAUUUUCCUCU
........(((((((((((((((((((.((((((.........(((.....)))....)))))).).)))))))))))))....)))))......................... (-19.34 = -19.14 +  -0.20)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 01:13:34 2011